PepSeq analysis for MHC II for C038_0038 and C038_0044

Patient Alleles:

Alleles on PepSeq run:

Var1 Freq
HLA-DQB1*02:01 18
HLA-DQB1*03:03 18
HLA-DQB1*05:01 6
HLA-DQB1*06:02 6
HLA-DQB1*06:03 6
HLA-DRB1*01:01 18
HLA-DRB1*03:01 18
HLA-DRB1*03:02 18
HLA-DRB1*11:04 18
HLA-DRB1*13:01 18
HLA-DRB1*13:02 18

Patient C038_0038

Alleles for Patient C038_0038:

patient_C038_0038_alleles
HLA-DQB1*03:01 (not run)
HLA-DRB1*11:04
HLA-DRB1*03:02 (This DR is named like the DQ’s?)

Select only mutant peptides?

HLA-DRB1*11:04 for patient C038_0038

## [1] "Replicates used: Un_1_11.04_ProG.L243_TM2_Norm48.A,B and Cl_1_11.04_ProG.L243_TM2_Norm48.B,C"

HLA-DRB1*03:02 for patient C038_0038 using 10uL.48 conditions.

## [1] "Replicates used: Un_1_03.02_ProG.L243_TM2_10uL.48_A,B,C and Cl_1_03.02_ProG.L243_TM2_10uL.48_A,B,C"

HLA-DRB1*03:02 for patient C038_0038 using 3XPool.48 conditions.

## [1] "Replicates used: Cl_1_03.02_ProG.L243_TM2_3XPool.48_A,C and Un_1_03.02_ProG.L243_TM2_3XPool.48_A,B"

Final MHC II pools for C038_0038

Using 3XPool.48 for HLA-DRB1*0302 peptides.

Patient C038_0044

Alleles for C038_0044:

patient_C038_0038_alleles
HLA-DQB1*03:03
HLA-DQB1*06:02
HLA-DRB1*07:01? (not on run)
HLA-DRB1*15:01? (not on run)

HLA-DQB1*03:03 for patient C038_0044 

## [1] "Replicates used: Un_QB_1_03.03_ProG.WR18.DR.DP.DQ_TM2_A,B,C and Cl_QB_1_03.03_ProG.WR18.DR.DP.DQ_TM2_A,C"

HLA-DQB1*06:02 for patient C038_0044 

## [1] "Replicates used: Un_QB_1_06.02_ProG.DQ_TM2_A,B,C and Cl_QB_1_06.02_ProG.DQ_TM2_A,C"

Final MHC II pools for C038_0044